cvJupyter

Summary¶

Brian Caffo, PhD is a professor in the Department of Biostatistics with a secondary appointment in the Department of Biomedical Engineering at Johns Hopkins University. He graduated from the University of Florida Department of Statistics in 2001. He has worked in statistical computing, statistical modeling, computational statistics, multivariate and decomposition methods and statistics in neuroimaging and neuroscience. He led teams that won the ADHD 200 prediction competition. He co-directs the SMART statistical group. With other faculty at JHU, he created and co-directs the Coursera Data Science Specialization, a 10 course specialization on statistical data analysis. He co-directs the JHU Data Science Lab, a group dedicated to open educational innovation and data science. He is the former director of the Biostatistics graduate programs and admissions committees. He is currently the co-director of the Johns Hopkins High Performance Computing Exchange super computing service center and president of the Bloomberg School of Public Health faculty senate.

Education¶

Year	Description	Institution
2006	K25 training grant	NIH	A mentored training program in imaging science'' emphasizing research and coursework in medical imaging
2001	PhD in statistics	U of Florida	Candidate sampling schemes and some important applications
1998	MS in statistics	U of Florida
1995	Dual BS in mathematics and statistics	U of Florida

Professional experience¶

Year	Title	Place
2019 -	Secondary	Dept of Biomedical Engineering, JHU
2019 -	Co-director	Johns Hopkins High Performance Computing Exchange (JHPCE)
2016 -	Faculty member	Kavli Neuroscience Discovery Institute
2017 -	Faculty member	Malone Center for Engineering and Healthcare
2014 -	Co-founding member	Johns Hopkins Data Science Lab
2011 -	Founding co-director	SMART research group
2013 -	Full professor	Dept of Biostat,JHU
2007-2013	Associate professor	Dept of Biostat,JHU
2001-2007	Assistant professor	Dept of Biostat,JHU
1996-1999	Research assistant for professor Alan Agresti	Department of Stat, UFL
1996, 1999	Intern / programmer	the Pediatric Oncology Group Statistical Office

Profesional activities¶

Typically two NIH, NSF or EU review panels per year
Publications Officer for the Biometrics Section of the American Statistical Association 2005-2006
Founding member (2010) and secretary (2010-) for the Statistics in Imaging ASA section
Typically oranizing 1 or 2 ENAR or JSM sessions per year
2006-2008 Associate editor Computational Statistics and Data Analysis
2008-2010 Associate editor for the Journal of the American Statistical Association
2009-2012 Associate editor for the Journal of the Royal Statistical Society Series B
2010-2012 Associate editor for Biometrics
Senior program committee member for the Fourteenth International Conference on Artificial Intelligence and Statistics
Guest associate editor for Frontiers in Neuroscience special issues on Brain Imaging Methods and Explainable Artificial Intelligence in Healthcare and Finance

Honors and awards¶

1998, William S. Mendenhall Award
1999, Anderson Scholar/Faculty nominee for the University of Florida CLAS
2001, University of Florida CLAS Dissertation Fellowship
2001, University of Florida Statistics Faculty Award
2002, Johns Hopkins Faculty Innovation Award
2006, Johns Hopkins Bloomberg School of Public Health AMTRA award
2008, Johns Hopkins Bloomberg School of Public Health Golden Apple teaching award
2011, Leader and organizer of the declared winning entry of the 2011 ADHD200 prediction competition
2011 Presidential Early Career Award for Scientists and Engineers (PECASE, 2010, awarded in 2011); The highest honor bestowed by the United States government on science and engineering professionals in the early stages of their independent research careers
2014, Named a Fellow of the American Statistical Association
2015, Special Invited Lecturer, European Meeting of Statisticians

Publications¶

Publications reported in Scopus as of 01/04/2021. My total number of Scopus publications is 228. Consider a plot of publication quantity by year. Clearly, the period from 2011 to 2012 was my productivity high water mark with 46 publications in 2 years.

Here are journals I publish in the most (4 or more times). Some journals I really like, and have published in, but (sadly) didn't make it to this list include JRSSA (1), JRSSB (2), JRSSC (1), Biometrika (1), IEEE TMI (1), Neurology (2), JCGS (3), AJE (2), Brain (2), JAMA Neurology (2), JAMA (1) and Neuroimage Clinical (2).

	Title	Count
0	NeuroImage	16
2	Journal of the American Statistical Association	9
1	Biostatistics	9
3	Human Brain Mapping	7
4	Computational Statistics and Data Analysis	7
5	Annals of Applied Statistics	6
6	PLoS ONE	6
7	Statistics in Medicine	5
8	American Statistician	5
9	Progress in Biomedical Optics and Imaging - Pr...	4
10	AIDS Research and Human Retroviruses	4
11	Sleep	4
12	Biometrics	4
13	American Journal of Neuroradiology	4

I have published with 625 coauthors. Here is a list of authors that I have had 10 or over manuscripts with.

	Author	Count
1	Crainiceanu C.	41
2	Pekar J.	28
3	Lindquist M.	23
4	Mostofsky S.	22
5	Hendrix C.	16
6	Punjabi N.M.	16
7	Nebel M.B.	15
8	Reich D.	14
9	Zhao Y.	13
10	Schwartz B.	11
11	Barber A.D.	11
12	Sair H.I.	11
13	Muschelli J.	11
14	Yousem D.	11
15	Eloyan A.	10

Here's a wordcloud of words in the titles (excluding common use words, in the shape of an axial brain slice).

Wordcloud

Here's the citation counts of manuscripts plotted by year of publication.

Part II¶

Advisees¶

2005 PhD Leena Choi, Johns Hopkins Biostatistics, Modelling biomedical data and the foundations of bioequivalence
2006 ScM Lijuan Deng, Johns Hopkins Biostatistics, Spline-based curve fitting with applications to kinetic imaging
2006 MS Bruce Swihart, University of Colorado Biostatistics, Quantitative characterization of sleep architecture using multi- state and log-linear models (jointly advised with Naresh Punjabi and Gary Grunwald)
2007 MPH Jeong Yun, Johns Hopkins Bloomberg School of Public Health, Incidence of hypertension in high risk groups of the Sleep Heart Health Study
2008 PhD Xianbin Li, Johns Hopkins Biostatistics, Modeling composite outcomes and their component parts
2008 PhD Shu-Chih Su, Johns Hopkins Biostatistics, Structure/function relationships in the analysis of anatomical and functional neuroimaging data
2010 ScM John Muschelli, Johns Hopkins Biostatistics, An iterative approach to hemodynamic response function temporal derivatives in statistical parametric mapping for functional neuroimaging
2011 PhD Haley Hedlin, Johns Hopkins Biostatistics, Statistical methods for inter-subject analysis of neuroscience data
2011 PhD Bruce Swihart, Johns Hopkins Biostatistics, From individuals to populations: application and insights concerning the generalized linear mixed model
2012 PhD Jeff Goldsmith (co-advised with primary advisor Ciprian Crainiceanu), Cross-Sectional and longitudinal penalized functional regression
2012 MPH Tiziano Marovino, The concurrent validity of musculo-skeletal ultrasound imaging in comparison to MRI for detecting rotator cuff tears in the shoulder when performed in a physical therapy setting
2013 ScM Rawan Al-Lozi, An evaluation of statistical modeling methods for predicting recovery time from post-traumatic amnesia following moderate or severe traumatic brain injury in children
2013 PhD Shanshan Li (co-advised with primary advisor Mei-Cheng Wang) Statistical Methods for Evaluating Diagnostic Accuracy of Biomarkers
2013 MHS Xiaoqiang Xu, Parallel Voxel Level Anything
2015 PhD Juemin Yang Statistical Methods for Brain Imaging and Genomic Data Analysis
2015 PhD Shaojie Chen Statistical Methods to Analyze Massive High-Dimensional Neuroimaging Data
2015 PhD Fang Han (Co-advised with Han Liu) Large-scale nonparametric and semiparametric inference for large complex and noisy datasets
2016 PhD Chen Yue (co-advised with Vadim Zipunnikov) Generalizations, extensions and applications for principal component analysis
2016 PhD Amanda Mejia (co-advised with primary advisor Martin Lindquist) Statistical Methods for Functional Magnetic Resonance Imaging Data
2016 PhD Aaron Fisher Methods for High Dimensional Analysis, Multiple Testing, and Visual Exploration
2016 PhD Huitong Qiu Statistical Methods and Theory for Analyzing High Dimensional Time Series
2020 PhD Zeyi Wang Statistical Analysis of Functional Connectivity in Brain Imaging: Measurement Reliability and Clinical Applications
2020 MSE Luchao Qi Associations between Body Mass Index (BMI) and Physical Activity: National Health and Nutritional Examination Survey (NHANES) 2005-2006
2021 PhD Bingkai Wang (co-advised with primary advisor Michael Rosenblum) Statistical Methods for Analyzing Randomized Trials and Brain Imaging Data

Post doctoral advisees¶

2009-2012 Vadim Zipunnikov (co-advising with primary advisor Ciprian Crainiceanu)
2010-2013 Ani Eloyan (co-advising with Ciprian Crainiceanu)
2011-2013 Seonjoo Lee (co-advising with primary advisor Dzung Pham)
2017-2020 Yi Zhao (co-advising with Stewart Mostofsky and Martin Lindquist)
2017-2020 Heather Shappell (co-advising with Jim Pekar and primary advisor Martin Lindquist)

Advisees in progress¶

Huan Chen
Bohao Tang
Eric Bridgeford (primary advisor Joshua Vogelstein)

Master's thesis reader¶

2021 Yuki Kang (Biostat), Xuemin Zhu (Biostat)
2020 Luchao Qi (Biostat)
2014 Clair Rock (U MD Epi)
2012 Rawan Al-Lozi, Francisco Leva
2011 Jiawei Bai (Biostat), Pohan Chen (Biostat)
2010 Ben Althouse (Biostat)
2009 Catherine Thomas (Biostat), Ros Reside (Epi)
2006 Ricardo Carvalho (GTPCI), Bruce Swihart (UC Denver Biostatistics)
2005 Brendan Click (Biostat), Jennifer Ryea (Biostat)
2004 Meh Fen Yeh (Biostat)

Student exam participation¶

Classroom Instruction¶

JHU¶

2001-2005 Primary instructor, Advanced Statistical Computing
2003-2004 Primary instructor, Advanced Methods in Biostatistics IV
2003-2004 Guest lecturer, Advanced Methods in Biostatistics II
2003-2008 Guest lecturer, Computing orientation and student computing club
2003-2004 2008 primary instructor, Statistical Computing
2004-2005 Primary instructor, Advanced Methods in Biostatistics III
2005-2010 Primary instructor, Methods in Biostatistics I
2005-2010 Primary instructor, Methods in Biostatistics II
2008 Primary instructor, Medical Imaging Statistics, Biostatistics PhD and ScM elective
2010-2017 Guest lecturer, Public Health Perspectives Biostatistics Module
2011-2014 Primary instructor, Advanced Methods in Biostatistics I and II
2013 Guest instructor, ICTR training program
2015-2018 Primary instructor, Advanced Linear Models I and II
2019-2021 Primary instructor, Introduction to Data Science for Biomedical Engineering

Short courses¶

2011 ENAR Statistical methods for new high throughput technological measurements; with Ciprian Crainiceanu
2015 Data Science Hackathon Co-organizer with Leah Jager, Jeff Leek and Roger Peng. Funded by the NIH
2017-2019 quarterly MRICloud and R Johns Hopkins tutorial series

Open Education¶

Coursera¶

Mathematical Biostatistics Boot Camp - 7 week course
Mathematical Biostatistics Boot Camp 2 - 7 week courses
Advanced Linear Models for Data Science 1: Least Squares
Advanced Linear Models for Data Science 2: Statistical Linear Models
Data Science Specialization (with Roger Peng and Jeff Leek); 9 one month classes run monthly plus a capstone project class; primary instructor for:
- Statistical Inference
- Regression Models
- Developing Data Products
Executive Data Science Specialization (with Roger Peng and Jeff Leek); 4 one month classes plus a capstone project
PI (roll of executive producer, non-instructor) for the BD2K R25 Genomic Data Science Specialization, fMRI 1 and 2 (Lindquist / Wager), Neurohacking in R (Craininceanu, Sweeney, Muschelli), Neuroscience for Neuroimaging (Baker)

E-books¶

Statistical Inference
Regression Models
Developing Data Products
Advanced Linear Models for Data Science
Methods in Biostatistics with R (with John Muschelli and Ciprian Crainiceanu)
Executive Data Science (with Roger Peng and Jeff Leek)

Other¶

swirl: Mentored project by Nick Carchedi intiated during his internship
Course notes for Biostatistics 140.651-2 listed on the Johns Hopkins Open Courseware project

Research support, PI grants¶

8/27/12 - 8/26/14 Johns Hopkins Brain Science Institute The Center for Quantitative Neuroscience: a core for population neuroanalytics and translational systems neuroscience as part of the RFA Traumatic brain injury: mechanisms and treatment
09/30/2010-8/31/2014 NIH NIBIB R01 EB012547 Statistical methods for hierarchical large n large p problems
05/01/06-04/30/09 NIH NIBIB K25 EB003491 A mentored training program in imaging science
12/01/14-11/30/17 NIH R25EB020378 Big Data Education for the Masses: MOOCs, Modules and Intelligent Tutoring Systems
09/01/11- 08/31/16 NIH NIBIB P41 EB015909 Resource for quantitative functional MRI R01 component of a P41 grant. R01 PIs Caffo/Pekar, P41 PI Van Zijl.
3/14/2012-3/14/2014 Amazon AWS Research Grant for Cloud Development of Neuroimaging Software.
8/16/2019 NVIDIA hardware grant

Co-investigator awards¶

Available by request

JHU major academic service¶

JHPCE Co-director 2019-
Malone Center director search committee 2021/2022
JHSPH Faculty senate president-elect 2019-2020
JHSPH Honors and Awards committee 2017-2019
JHSPH Faculty Innovation Fund grant referee 2017 - 2018
BME faculty hiring committee 2016
Biostat faculty hiring committee 2016
Malone Center Steering Committee 2016 -
Biostatistics admissions committee member 2002 - 2009, 2010 -
Biostatistics co-director of the graduate program 2010 - 2012
Biostatistics director of the graduate program 2012 - 2016
Biostatistics information technology committee member 2001 - 2009
Biostatistics seminar coordinator 2001 - 2002
Co-director Biostatistics/Epidemiology MPH concentration 2008 - 2010
Co-organizer Junior Faculty Meetings 2003
CEDC (originally Committee on Affirmative Action) member 2007 - 2010
Faculty Senate representative 2002 - 2004
MPH Admissions Committee member 2009 - 2011
MPH Executive Board member 2009 - 2011

Brian S Caffo¶